The issue is that this plugin was never designed to be placed at the end of the plugin stack. It was always intended that other plugins would be run after it.
That being said, rather than me telling you to modify your config, I decided to update that plugin with some much needed improvements.
I've pushed an update (v0.0.4) for that plugin that should give you a few more options. If you update the plugin on your install it should solve your issues. I have also re-written the description a bit, so take a look at that as there is now a new config option.
Let me know if it works for you...